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- PDB-8dxd: [C:Hg2+/Ag+:C--pH 8] Metal-mediated DNA base pair in tensegrity t... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dxd | |||||||||||||||||||||
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Title | [C:Hg2+/Ag+:C--pH 8] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution | |||||||||||||||||||||
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Function / homology | : / ![]() ![]() | |||||||||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Lu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P. | |||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals. Authors: Lu, B. / Ohayon, Y.P. / Woloszyn, K. / Yang, C.F. / Yoder, J.B. / Rothschild, L.J. / Wind, S.J. / Hendrickson, W.A. / Mao, C. / Seeman, N.C. / Canary, J.W. / Sha, R. / Vecchioni, S. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.5 KB | Display | ![]() |
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PDB format | ![]() | 42.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7slbC ![]() 7slcC ![]() 7sldC ![]() 7sleC ![]() 7slfC ![]() 7slgC ![]() 7sljC ![]() 7slkC ![]() 7sllC ![]() 7slmC ![]() 7slnC ![]() 7sloC ![]() 7sm0C ![]() 7sm1C ![]() 7sm2C ![]() 7sm3C ![]() 7sm4C ![]() 7sm5C ![]() 7sm6C ![]() 7sm7C ![]() 7sm8C ![]() 7sm9C ![]() 7smaC ![]() 7smbC ![]() 7ti3C ![]() 7ujzC ![]() 7uk0C ![]() 8dx1C ![]() 8dx5C ![]() 8dx6C ![]() 8dx7C ![]() 8dx9C ![]() 8dxaC ![]() 8dxcC ![]() 8dxfC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 6448.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 2051.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: Chemical | ChemComp-HG / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 7.82 Å3/Da / Density % sol: 84.28 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 40 mM Tris, 125 mM Magnesium sulfate, 12 uM silver nitrate, 24 uM mercury chloride Temp details: 338-293 at 0.4/hr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 4.28→65.23 Å / Num. obs: 3486 / % possible obs: 83.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 310.4 Å2 / CC1/2: 1 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 4.28→4.88 Å / Num. unique obs: 386 / CC1/2: 0.09 |
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Processing
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Refinement | Method to determine structure![]() ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 358.1 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.28→32.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.28→32.61 Å
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